[gmx-users] I have a problem with my biphasic system
jalemkul at vt.edu
Thu Nov 1 23:07:16 CET 2012
On 11/1/12 5:49 PM, Ali Alizadeh wrote:
> Dear All usres
> I have a system that contains water , methane and propane in 240 k and 300
> My simulation box is rectangular .
> Water film is in middle of my box. Methane and propane is around it.
> I have a problem, my methane and propane molecules do not diffuse in water
> film(even my methane molecules),
> I do simulation, 30 nano second
> methane molecules = 834
> propane molecules = 92
> water molecules = 1656
> These links is related to md.mdp and .mdp for energy minimization
The permissions on your files are set such that no one else can view them.
Why would you expect your alkanes to dissolve in water? The solubility of
methane is very small (roughly 0.02 g/kg of water at 25 C, or about 0.0014 M).
Given this information, in your very small system, basically no methane
molecules would ever partition into the water layer. I didn't do the
back-of-the-envelope calculations for propane, but you get the idea.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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